The government is to take the controversial and potentially unpopular step of scrapping four-hour waiting time targets in accident and emergency departments and instead focus on delivering the "best possible results for patients", it said yesterday.

The coalition government had already announced widespread cuts to NHS targets that have "no clinical justification" without stipulating where the axe was likely to fall. But yesterday the health secretary, Andrew Lansley, revealed the plan as he took questions in the House of Commons following his announcement of a full public inquiry into failings at Mid-Staffordshire NHS Foundation Trust.

"We are going to look, and we will look constructively, at how we can scrap the four-hour target as it currently exists and work on the basis of what the clinical evidence makes clear directly contributes to delivering the best possible results for patients," said Lansley.

Asked to clarify his remarks, he said: "I was very clear in what I had to say – I'm going to abolish the four-hour A&E target. I will issue guidance to the NHS shortly, the purpose of which … is in order to ensure that we deliver better quality."

The news was cautiously welcomed in some areas. Mark Porter, chairman of the The British Medical Association's Consultants Committee, said that it was vital that patients were treated on the basis of their clinical need.

"Waiting time targets – by focusing attention on every patient – have improved the NHS in many respects. However, in some cases they have also created pressure on staff to make inappropriate decisions that could compromise care," he said.

Katherine Murphy, director of the Patients Association, said that targets had caused problems as managers focused on financial gain rather than clinical outcomes, but they had to be replaced with benchmarks and a system that regularly assessed patient experience. "There does need to be rigour in the system otherwise we could go back to the days when people were waiting on trolleys for two or three days," she said.

The shadow health secretary, Andy Burnham, said abolishing this target would be a major backward step for the NHS. "It opens the door to a return to the bad old days when patients spent hours on end waiting to be seen," he said. "Now Andrew Lansley urgently needs to give clarity to the NHS by explaining what alternative plans he has."

Lansley said that lower waiting times were "not a measure of the result for patients" as had been shown at Stafford hospital where between 400 and 1,200 more people died than would have been expected over three years.

"What happened at Stafford was evidence, and we had other evidence in many other places, that the four-hour target was being pursued not in order to give the best possible care to patients – but in spite of what would be the best possible care for patients," he told MPs.

He announced that a public inquiry into the unnecessary deaths of at least 400 patients at Stafford hospital, which had been rejected by the Labour government, would question senior NHS officials at the hospital's trust, as well as the local and national NHS bodies.

Regulators found a catalogue of failings including poor accident and emergency care, bad hygiene, and patients being helped by relatives because staff were too busy.

Lansley said: "Why did the primary care trust and strategic health authority not see what was happening and intervene earlier?"

The inquiry will be headed by Robert Francis QC, who undertook an independent inquiry into the scandal for the Labour government and produced a damning report in February. Unlike his first inquiry, Francis will this time hold hearings in public and have the power to compel witnesses to attend and answer questions.